[gmx-users] Different g_sas values between AMBER, CHARMM and GROMOS ff for DPC
sagmx.mail at gmail.com
Sun Apr 10 11:11:28 CEST 2011
Thank you David,
My micelle simulated with the GROMOS ff slightly differs (size and shape)
from the two others micelles, so i expected that the values total SAS value
slightly differ. In case of the headgroup, they are located in the micelle
interface region, so the SAS in case of the micelle simulated with GROMOS
should be not so different (36 % less) than the others micelles
You said that "In order for g_sas to work with gromos force field one would
increase the radius of the carbon atoms. For the 54 atoms the default
value will be used." How to do that ? and for all the carbon atoms
(including the headgroup carbon atoms).
> On 2011-04-09 19.06, sa wrote:
> > Dear All,
> > I have simulated three DPC micelles with the same size (54 lipids) with
> > different force fields (CHARMM, AMBER et GROMOS53A6) and computed the
> > average accessible surface areas for each lipids with g_sas (gmx4.5.3) I
> > obtain the three average values for total DPC, the headgroup
> > (phosphocholine) and the alkyl tail.
> > Total (A2) Head Tail
> > GROMOS53A6 158.4 ± 4.8 54.8 ± 3.4 103.2 ± 3.8
> > AMBER 248.2 ± 8.7 76.2 ± 5.1 172.5 ± 5.2
> > CHARMM 242.7 ± 7.7 70.4 ± 4.1 172.4 ± 4.8
> > As you can see the ASA values are close between the micelles simulated
> > with the CHARMM and AMBER ff, but larger than the values obtained from
> > the micelle simulated with GROMOS ff especially for the headgroup. I am
> > aware that CHARMM and AMBER are explicits ff whereas GROMOS is an
> > united ff It is the reason I obtain a smaller values for GROMOS
> > compared to two others ones ?
> > Does g_sas tool take into account this. I have also noted when I use
> > g_sas i obtain the following message
> > WARNING: masses and atomic (Van der Waals) radii will be determined
> > based on residue and atom names. These numbers can deviate
> > from the correct mass and radius of the atom type.
> > WARNING: could not find a Van der Waals radius for 54 atoms
> > It is important ?
> Given your observations above, don't you think it might be?
> In order for g_sas to work with gromos force field one would have to
> increase the radius of the carbon atoms. For the 54 atoms the default
> value will be used.
> > Thank you in advance for your advices.
> > SA
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
> spoel at xray.bmc.uu.se http://folding.bmc.uu.se
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